Contacts of the helix formed by residues 144 - 153 (chain A) in PDB entry 3SMZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.1 15.0 - - - +
142A SER 3.7 12.3 - - - +
143A LEU* 1.3 78.9 - - - +
145A GLN* 1.3 59.0 + - - +
146A GLN* 3.6 8.4 + - - +
147A GLN* 3.1 35.4 + - - +
148A PHE* 2.9 25.6 + - - +
163A LEU* 3.6 3.4 - - - -
165A TYR* 6.3 0.4 - - - -
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Residues in contact with GLN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 3.7 27.9 + - + +
51A THR* 4.8 2.1 + - - -
144A THR* 1.3 72.9 - - - +
146A GLN* 1.3 57.7 + - - +
148A PHE* 3.2 3.0 + - - +
149A GLU* 2.8 63.5 + - - +
161A CYS* 3.0 27.7 + - - -
162A PHE* 3.4 2.9 - - - +
163A LEU* 2.9 40.8 + - - +
165A TYR* 3.4 19.8 + - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A THR* 3.3 7.5 + - - +
145A GLN* 1.3 78.6 - - - +
147A GLN* 1.3 61.1 + - - +
149A GLU* 3.4 16.7 + - - +
150A GLU* 3.0 57.6 + - + +
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER 4.2 1.6 - - - +
143A LEU* 3.6 28.5 - - + +
144A THR* 3.1 39.8 + - - +
146A GLN* 1.3 79.8 - - + +
148A PHE* 1.4 57.8 + - - +
150A GLU* 3.3 17.0 + - - +
151A LEU* 3.0 27.4 + - - +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.7 30.3 - - + -
139A LEU* 3.8 21.1 - - + -
143A LEU* 3.6 10.5 - - + +
144A THR 2.9 13.8 + - - +
145A GLN* 3.2 8.5 + - - +
147A GLN* 1.4 74.2 - - - +
149A GLU* 1.3 62.3 + - - +
151A LEU* 3.2 14.8 + - + +
152A VAL* 3.2 37.4 + - + +
161A CYS* 3.7 22.0 - - - -
162A PHE* 3.8 8.5 - - - -
163A LEU* 3.7 19.1 - - + -
176A GLY* 3.6 23.6 - - - -
177A PHE 3.6 30.5 - - - -
178A ALA* 4.5 0.4 - - + -
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 3.8 12.0 + - - -
54A GLN* 5.7 0.5 + - - -
145A GLN* 2.8 50.6 + - - +
146A GLN* 3.6 17.0 - - - +
148A PHE* 1.3 75.0 - - - +
150A GLU* 1.4 60.1 + - + +
152A VAL* 3.8 0.6 - - - +
153A ARG* 2.8 38.4 + - + +
158A LEU* 5.3 2.9 - - + -
161A CYS* 3.6 22.4 - - + +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLN* 3.0 49.1 + - + +
147A GLN* 3.7 17.8 - - - +
148A PHE 3.3 0.2 - - - -
149A GLU* 1.4 77.5 - - + +
151A LEU* 1.3 58.8 + - - +
153A ARG* 4.8 3.4 - - - -
154A PRO* 3.3 19.8 - - - +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 4.6 0.9 - - + -
139A LEU* 4.1 25.6 - - + -
143A LEU* 5.7 3.1 - - + -
147A GLN 3.0 13.2 + - - +
148A PHE* 3.4 21.1 - - + +
149A GLU 3.2 0.4 - - - -
150A GLU* 1.3 78.8 - - - +
152A VAL* 1.3 59.2 + - + +
154A PRO* 3.5 10.6 - - - +
155A PHE* 3.6 15.6 - - - -
193A LEU* 3.8 31.4 - - + +
196A LYS* 3.9 21.5 - - + -
198A LEU* 4.4 13.9 - - + -
203A LEU* 4.1 13.0 - - + -
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 6.6 0.2 - - + -
136A VAL* 4.3 2.9 - - + -
148A PHE* 3.2 38.3 + - + +
149A GLU 3.8 2.2 - - - +
151A LEU* 1.3 79.1 - - + +
153A ARG* 1.4 65.8 + - - +
154A PRO* 3.3 3.6 - - - -
155A PHE* 3.3 13.2 + - - -
158A LEU* 4.0 7.4 - - + -
161A CYS* 3.7 24.2 - - - -
178A ALA* 4.0 19.1 - - + -
180A TYR* 2.6 33.6 + - - +
193A LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLU* 2.8 26.6 + - + +
150A GLU* 4.8 2.7 - - - -
152A VAL* 1.4 73.8 - - - +
154A PRO* 1.4 65.4 + - + +
155A PHE 3.0 1.6 + - - -
156A GLY* 3.2 29.0 + - - +
157A SER* 3.5 24.0 - - - +
158A LEU* 3.8 20.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il